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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagttctcttttttaataaatttttaccttgaatttagctgtttttttagcaatcttggtttcacaactatgctttctgttttgctaacagCTGCAATTGTACTTCAAGCCAAGGCCGCCAGAAGGTAGTAAACCACCACCAGCTCCTCCTGGAACTTTGCCTAATGGGACTGGGGCTCCTGGTGCTCCAC

Basic information

species Zea mays
transcript GRMZM2G100620_T01
intron # 6
splice site 3'
intron type U2

Mapped EST sequences

Showing partial alignments of ESTs and genomic sequences. See full alignments


 ATGC     EST sequence
 ATGC     genomic sequence (exon)
 ATGC     genomic sequence (truncated intron)


EST: gi|60341101|gb|DN208074.1|DN208074
EST:     CAGCGAGCAAATTCTTCTCTTACTGGGATCCTGACAAGAAGGAATACCTG                         CTGCAATTGTACTTCAAGCCAAGGCCGCCAGAAGGTAGTAAACCACCACCA
genomic: CAGCGAGCAAATTCTTCTCTTACTGGGATCCTGACAAGAAGGAATACCTGgtgagttctc ... ttgctaacagCTGCAATTGTACTTCAAGCCAAGGCCGCCAGAAGGTAGTAAACCACCACCA
EST: gi|211471653|gb|FL177820.1|FL177820
EST:     CAGCGAGCAAATTCTTCTCTTACTGGGATCCTGACAAGAAGGAATACCTG                         CTGCAATTGTACTTCAAGCCAAGGCCGCCAGAAGGTAGTAAACCACCACCA
genomic: CAGCGAGCAAATTCTTCTCTTACTGGGATCCTGACAAGAAGGAATACCTGgtgagttctc ... ttgctaacagCTGCAATTGTACTTCAAGCCAAGGCCGCCAGAAGGTAGTAAACCACCACCA
EST: gi|149014483|gb|EE044106.2|EE044106
EST:     CAGCGAGCAAATTCTTCTCTTACTGGGATCCTGACAAGAAGGAATACCTG                         CTGCAATTGTACTTCAAGCCAAGGCCGCCAGAAGGTAGTAAACCACCACCA
genomic: CAGCGAGCAAATTCTTCTCTTACTGGGATCCTGACAAGAAGGAATACCTGgtgagttctc ... ttgctaacagCTGCAATTGTACTTCAAGCCAAGGCCGCCAGAAGGTAGTAAACCACCACCA
EST: gi|19272503|gb|BM888759.1|BM888759
EST:     CAGCGAGCAAATTCTTCTCTTACTGGGATCCTGACAAGAAGGAATACCTG                         CTGCAATTGTACTTCAAGCCAAGGCCGCCAGAAGGTAGTAAACCACCACCA
genomic: CAGCGAGCAAATTCTTCTCTTACTGGGATCCTGACAAGAAGGAATACCTGgtgagttctc ... ttgctaacagCTGCAATTGTACTTCAAGCCAAGGCCGCCAGAAGGTAGTAAACCACCACCA
EST: gi|149111001|gb|EE294500.2|EE294500
EST:     CAGCGAGCAAATTCTTCTCTTACTGGGATCCTGACAAGAAGGAATACCTG                         CTGCAATTGTACTTCAAGCCAAGGCCGCCAGAAGGTAGTAAACCACCACCA
genomic: CAGCGAGCAAATTCTTCTCTTACTGGGATCCTGACAAGAAGGAATACCTGgtgagttctc ... ttgctaacagCTGCAATTGTACTTCAAGCCAAGGCCGCCAGAAGGTAGTAAACCACCACCA
EST: gi|91056062|gb|EB166480.1|EB166480
EST:     CAGCGAGCAAATTCTTCTCTTACTGGGATCCTGACAAGAAGGAATACCTG                         CTGCAATTGTACTTCAAGCCAAGGCCGCCAGAAGGTAGTAAACCACCACCA
genomic: CAGCGAGCAAATTCTTCTCTTACTGGGATCCTGACAAGAAGGAATACCTGgtgagttctc ... ttgctaacagCTGCAATTGTACTTCAAGCCAAGGCCGCCAGAAGGTAGTAAACCACCACCA
EST: gi|76292130|gb|DV031698.1|DV031698
EST:     CAGCGAGCAAATTCTTCTCTTACTGGGATCCTGACAAGAAGGAATACCTG                         CTGCAACTGTACTTCAAGCCAAGGCCGCCAGAAGGTAGTAAACCACCACCA
genomic: CAGCGAGCAAATTCTTCTCTTACTGGGATCCTGACAAGAAGGAATACCTGgtgagttctc ... ttgctaacagCTGCAATTGTACTTCAAGCCAAGGCCGCCAGAAGGTAGTAAACCACCACCA
EST: gi|148944813|gb|EC889958.2|EC889958
EST:     CAGCGAGCAAATTCTTCTCTTACTGGGATCCTGACAAGAAGGAATACCTG                         CTGCAATTGTACTTCAAGCCAAGGCCGCCAGAAGGTAGTAAACCACCACCA
genomic: CAGCGAGCAAATTCTTCTCTTACTGGGATCCTGACAAGAAGGAATACCTGgtgagttctc ... ttgctaacagCTGCAATTGTACTTCAAGCCAAGGCCGCCAGAAGGTAGTAAACCACCACCA
EST: gi|78092801|gb|DV521175.1|DV521175
EST:     CAGCGAGCAAATTCTTCTCTTACTGGGATCCTGACAAGAAGGAATACCTG                         CTGCAATTGTACTTCAAGCCAAGGCCGCCAGAAGGTAGTAAACCACCACCA
genomic: CAGCGAGCAAATTCTTCTCTTACTGGGATCCTGACAAGAAGGAATACCTGgtgagttctc ... ttgctaacagCTGCAATTGTACTTCAAGCCAAGGCCGCCAGAAGGTAGTAAACCACCACCA
EST: gi|78077143|gb|DV505577.1|DV505577
EST:     CAGCGAGCAAATTCTTCTCTTACTGGGATCCTGACAAGAAGGAATACCTG                         CTGCAATTGTACTTCAAGCCAAGGCCGCCAGAAGGTAGTAAACCACCACCA
genomic: CAGCGAGCAAATTCTTCTCTTACTGGGATCCTGACAAGAAGGAATACCTGgtgagttctc ... ttgctaacagCTGCAATTGTACTTCAAGCCAAGGCCGCCAGAAGGTAGTAAACCACCACCA
EST: gi|148937013|gb|EC881184.2|EC881184
EST:     CAGCGAGCAAATTCTTCTCTTACTGGGATCCTGACAAGAAGGAATACCTG                         CTGCAATTGTACTTCAAGCCAAGGCCGCCAGAAGGTAGTAAACCACCACCA
genomic: CAGCGAGCAAATTCTTCTCTTACTGGGATCCTGACAAGAAGGAATACCTGgtgagttctc ... ttgctaacagCTGCAATTGTACTTCAAGCCAAGGCCGCCAGAAGGTAGTAAACCACCACCA
EST: gi|71439882|gb|DR820932.1|DR820932
EST:     CAGCGAGCAAATTCTTCTCTTACTGGGATCCTGACAAGAAGGAATACCTG                         CTGCAATTGTACTTCAAGCCAAGGCCGCCAGAAGGTAGTAAACCACCACCA
genomic: CAGCGAGCAAATTCTTCTCTTACTGGGATCCTGACAAGAAGGAATACCTGgtgagttctc ... ttgctaacagCTGCAATTGTACTTCAAGCCAAGGCCGCCAGAAGGTAGTAAACCACCACCA
EST: gi|149111002|gb|EE294501.2|EE294501
EST:     CAGCGAGCAAATTCTTCTCTTACTGGGATCCTGACAAGAAGGAATACCTG                         CTGCAATTGTACTTCAAGCCAAGGCCGCCAGAAGGTAGTAAACCACCACCA
genomic: CAGCGAGCAAATTCTTCTCTTACTGGGATCCTGACAAGAAGGAATACCTGgtgagttctc ... ttgctaacagCTGCAATTGTACTTCAAGCCAAGGCCGCCAGAAGGTAGTAAACCACCACCA
EST: gi|18654690|gb|BM499495.1|BM499495
EST:     CAGCGAGCAAATTCTTCTCTTACTGGGATCCTGACAAGAAGGAATACCTG                         CTGCAATTGTACTTCAAGCCAAGGCCGCCAGAAGGTAGTAAACCACCACCA
genomic: CAGCGAGCAAATTCTTCTCTTACTGGGATCCTGACAAGAAGGAATACCTGgtgagttctc ... ttgctaacagCTGCAATTGTACTTCAAGCCAAGGCCGCCAGAAGGTAGTAAACCACCACCA
EST: gi|50330974|gb|CO526100.1|CO526100
EST:     CAGCGAGCAAATTCTTCTCTTACTGGGATCCTGACAAGAAGGAATACCTG                         CTGCAATTGTACTTCAAGCCAAGGCCGCCAGAAGGTAGTAAACCACCACCA
genomic: CAGCGAGCAAATTCTTCTCTTACTGGGATCCTGACAAGAAGGAATACCTGgtgagttctc ... ttgctaacagCTGCAATTGTACTTCAAGCCAAGGCCGCCAGAAGGTAGTAAACCACCACCA
EST: gi|78113433|gb|DV531825.1|DV531825
EST:     CAGCGAGCAAATTCTTCTCTTACTGGGATCCTGACAAGAAGGAATACCTG                         CTGCAATTGTACTTCAAGCCAAGGCCGCCAGAAGGTAGTAAACCACCACCA
genomic: CAGCGAGCAAATTCTTCTCTTACTGGGATCCTGACAAGAAGGAATACCTGgtgagttctc ... ttgctaacagCTGCAATTGTACTTCAAGCCAAGGCCGCCAGAAGGTAGTAAACCACCACCA
EST: gi|6564142|gb|AW231764.1|AW231764
EST:     CAGCGAGCAAATTCTTCTCTTACTGGGATCCTGACAAGAAGGAATACCTG                         CTGCAATTGTACTTCAAGCCAAGGCCGC-AGAAGGTAGTAAACCACCACCA
genomic: CAGCGAGCAAATTCTTCTCTTACTGGGATCCTGACAAGAAGGAATACCTGgtgagttctc ... ttgctaacagCTGCAATTGTACTTCAAGCCAAGGCCGCCAGAAGGTAGTAAACCACCACCA
EST: gi|149081122|gb|EE170228.2|EE170228
EST:     CAGCGAGCAAATTCTTCTCTTACTGGGATCCTGACAAGAAGGAATACCTG                         CTGCAATTGTACTTCAAGCCAAGGCCGCCAGAAGGTAGTAAACCACCACCA
genomic: CAGCGAGCAAATTCTTCTCTTACTGGGATCCTGACAAGAAGGAATACCTGgtgagttctc ... ttgctaacagCTGCAATTGTACTTCAAGCCAAGGCCGCCAGAAGGTAGTAAACCACCACCA
EST: gi|19351666|gb|BM896198.1|BM896198
EST:     CAGCGAGCAAATTCTTCTCTTACTGGGATCCTGACAAGAAGGAATACCTG                         CTGCAATTGTACTTCAAGCCAAGGCCGCCAGAAGGTAGTAAACCACCACCA
genomic: CAGCGAGCAAATTCTTCTCTTACTGGGATCCTGACAAGAAGGAATACCTGgtgagttctc ... ttgctaacagCTGCAATTGTACTTCAAGCCAAGGCCGCCAGAAGGTAGTAAACCACCACCA
EST: gi|19351243|gb|BM895775.1|BM895775
EST:     CAGCGAGCAAATTCTTCTCTTACTGGGATCCTGACAAGAAGGAATACCTG                         CTGCAATTGTACTTCAAGCCAAGGCCGCCAGAAGGTAGTAAACCACCACCA
genomic: CAGCGAGCAAATTCTTCTCTTACTGGGATCCTGACAAGAAGGAATACCTGgtgagttctc ... ttgctaacagCTGCAATTGTACTTCAAGCCAAGGCCGCCAGAAGGTAGTAAACCACCACCA
EST: gi|211028537|gb|FL445303.1|FL445303
EST:     CAGCGAGCAAATTCTTCTCTTACTGGGATCCTGACAAGAAGGAATACCTG                         CTGCAATTGTACTTCAAGCCAAGGCCGCCAGAAGGTAGTAAACCACCACCA
genomic: CAGCGAGCAAATTCTTCTCTTACTGGGATCCTGACAAGAAGGAATACCTGgtgagttctc ... ttgctaacagCTGCAATTGTACTTCAAGCCAAGGCCGCCAGAAGGTAGTAAACCACCACCA

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 4 RNA-Seq libraries.


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 180

ATACCAAGTACAGAGATTGACAAATCAGCGAGCAAATTCTTCTCTTACTGGGATCCTGACAAGAAGGAATACCTGgtgagttctc ... ttgctaacagCTGCAATTGTACTTCAAGCCAAGGCCGCCAGAAGGTAGTAAACCACCACCAGCTCCTCCTGGAACTTTGCCTAATGGGACTGGGGCTCCTGGTGCTCCAC


Block sizes: 49 (upstream exon), 43 (downstream exon)
Score: 86

ATACCAAGTACAGAGATTGACAAATCAGCGAGCAAATTCTTCTCTTACTGGGATCCTGACAAGAAGGAATACCTGgtgagttctc ... ttgctaacagCTGCAATTGTACTTCAAGCCAAGGCCGCCAGAAGGTAGTAAACCACCACCAGCTCCTCCTGGAACTTTGCCTAATGGGACTGGGGCTCCTGGTGCTCCAC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 67

ATACCAAGTACAGAGATTGACAAATCAGCGAGCAAATTCTTCTCTTACTGGGATCCTGACAAGAAGGAATACCTGgtgagttctc ... ttgctaacagCTGCAATTGTACTTCAAGCCAAGGCCGCCAGAAGGTAGTAAACCACCACCAGCTCCTCCTGGAACTTTGCCTAATGGGACTGGGGCTCCTGGTGCTCCAC


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 111

ATACCAAGTACAGAGATTGACAAATCAGCGAGCAAATTCTTCTCTTACTGGGATCCTGACAAGAAGGAATACCTGgtgagttctc ... ttgctaacagCTGCAATTGTACTTCAAGCCAAGGCCGCCAGAAGGTAGTAAACCACCACCAGCTCCTCCTGGAACTTTGCCTAATGGGACTGGGGCTCCTGGTGCTCCAC




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agctgtttttttagcaatcttggtttcacaactatgctttctgttttgctaacagCTGCAATTGTACTTCAAGCCAAGGCCGCCAGAAGGTAGTAAACCACCACCAGCTCCTCCTGGAACTTTGCCTAATGGGACTGGGGCTCCTGGTGCTCCAC
                                    ctttctgttttgct  CT-rich tract
     ttttttta  TA-rich tract
















Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagttctcttttttaataaatttttaccttgaatttagctgtttttttagcaatcttggtttcacaactatgctttctgttttgctaacagCTGCAATTGTACTTCAAGCCAAGGCCGCCAGAAGGTAGTAAACCACCACCAGCTCCTCCTGGAACTTTGCCTAATGGGACTGGGGCTCCTGGTGCTCCAC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTCCTC